A total of 572 advanced intercross chickens were produced. Advanced intercross lines (AIL) were generated by crossing between one Red Junglefowl male (RJF) and three White Leghorn (WL) females. Maintaining both the phenotypic and genotypic diversity were the main focus during breeding of each generation.

At the age of 230 days all birds were sacrificed, whole wings were separated by surgically removing from shoulder joint. All wings were photographed using digital camera. Colour measurements were done in Adobe Photoshop CS4. A representative region of red and white colour of wing was selected using the Rectangular Marquee Tool. Colour density was then measured using the histogram function.

DNA preparation and genotyping for all birds were done in the laboratory at Linkoping University.  In this study a total of 657 molecular markers were used covering 30 autosomes and Z chromosome. In the current study, the total map distance covered 11228 centimorgan (cM) and the average interval distance is 17 cM

QTL analyses for red and metallic green pigmentations were performed using standard interval mapping through R/qtl. R/qtl is an adons of freely available statistical scripting language R and is specially designed for QTL analyses. Sex and batch were included as fixed factors in all QTL models. Additionally, all QTLs were also tested as sex interaction term.